Jian Zhong Zhang

Low-cost, high-sensitivity laser-induced fluorescence detection for DNA sequencing by capillary gel electrophoresis

A low cost, 0.75-mW helium neon laser, operating in the green region at 534.5 nm, is used to excite fluorescence from tetramethylrhodamine isothiocyanate-labelled DNA fragments that have been separated by capillary gel electrophoresis. The detection limit (3 sigma) for the dye is 500 ymol [1 yoctomole (1 ymol) = 10(-24) mol] or 300 analyte molecules in capillary zone electrophoresis; the detection limit for labeled primer separated by capillary gel electrophoresis is 2 zmol [1 zeptomole (1 zmol) = 10(-21) mol]. The Richardson-Tabor peak-height encoded sequencing technique is used to prepare DNA sequencing samples. In 6% T, 5% C acrylamide, 7 M urea gels, sequencing rates of 300 bases/hour are produced at an electric field strength of 200 V/cm; unfortunately, the data are plagued by compressions. These compressions are eliminated with addition of 20% formamide to the sequencing gel; the gel runs slowly and sequencing data are generated at a rate of about 70 bases/hour.

Attachment of a single fluorescent label to peptides for determination by capillary zone electrophoresis

Complicated electropherograms are produced in the separation of fluorescently labeled peptides. Incomplete labeling of epsilon-amino groups on lysine residues results in the production of 2n-1 reaction products, where n is the number of alpha and epsilon amino groups in the peptide. A single label is attached to the peptide by first taking the peptide through one cycle of the Edman degradation reaction. All epsilon-amino groups are converted to the phenyl thiocarbamyl and the cleavage step exposes one alpha-amino group at the N-terminus of the peptide; the fluorescent label is attached to the N-terminus.

Analysis by capillary electrophoresis-laser-induced fluorescence detection of oligosaccharides produced from enzyme reactions.

Six structurally similar, fluorescently labeled oligosaccharides were baseline resolved by capillary electrophoresis (CE); laser induced fluorescence (LIF) detection gave detection limits of 50 molecules for the oligosaccharides. A simple design of the LIF detector that incorporates the advantages of high sensitivity, stability and ease of operation is described. The system was used to monitor enzyme products formed during the incubation of yeast cells with alpha-D-Glc(1-->2)alpha-D-Glc(1-->3)alpha-D-glc-O(CH2)8CONHCH2CH2NHCO - tetramethylrhodamine. This fluorescent trisaccharide is enzymatically hydrolyzed to fluorescent disaccharide, monosaccharide and the free linker arm that is used to conjugate the saccharides with the fluorophore tetramethylrhodamine.

Construction and evaluation of a capillary array DNA sequencer based on a micromachined sheath-flow cuvette

A capillary array electrophoresis DNA sequencer is reported based on a micromachined sheath‐flow cuvette as the detection chamber. This cuvette is equipped with a set of micromachined features that hold the capillaries in precise registration to ensure uniform spacing between the capillaries, in order to generate uniform hydrodynamic flow in the cuvette. A laser beam excites all of the samples simultaneously, and a microscope objective images fluorescence onto a set of avalanche photodiodes, which operate in the analog mode. A high‐gain transimpedance amplifier is used for each photodiode, providing high duty‐cycle detection of fluorescence.

Effect of total percent polyacrylamide in capillary gel electrophoresis for DNA sequencing of short fragments. A phenomenological model.

Polyacrylamide capillary gels were prepared with constant (5% C) cross-linker concentration and with total acrylamide concentration ranging from 2.5 to 6% T. At each acrylamide concentration, peak spacing was constant for DNA sequencing fragments ranging from 25 to 250 nucleotides in length. Peak spacing increased linearly with the total acrylamide concentration. The intercept of the retention time vs. fragment length plot was independent of % T. Ferguson plots were constructed for short DNA fragments; the polyacrylamide pore size falls in the 2.5 to 3.5 nm range for the gels studied. Theoretical plate count is independent of total acrylamide concentration; longitudinal diffusion, and not thermal gradients, limit the plate count. A phenomenological model is presented that predicts retention time, plate count, and resolution for sequencing fragments ranging in size from 25 to 250 bases and gels that range from 2.5 to 6% total acrylamide.

Single-color laser-induced fluorescence detection and capillary gel electrophoresis for DNA sequencing

Low zeptomole (1 zmol equals 10-21 mol = 600 molecules) detection limits are produced for DNA sequencing by capillary gel electrophoresis. A 750 (mu) w green helium-neon laser ((lambda) equals 543.5 nm) is used to excite tetramethylrhodamine-labeled DNA fragments in a sheath-flow cuvette. A cooled photomultiplier tube is used to detect fluorescence in a single spectral channel. Sequencing data is generated at a rate of about 70 bases/hour.

Use of capillary electrophoresis to study methylation patterns in DNA

A four-color multiple capillary DNA sequencer is used to determine the methylation pattern of double stranded DNA. The DNA sample is treated with bisulfite under conditions that convert cytosine to uracil. Methyl-cytosine is inert under these reaction conditions. After PCR amplification, the reaction products are subjected to a four-color fluorescent Sanger sequencing reaction. The sequence is then determined by use of capillary electrophoresis. Comparison of the sequence obtained after bisulfite treatment with the original sequence reveals that certain of the Cs in the original sequence are converted to Ts. This conversion occurs only if the original C was not methylated. Those Cs that are common to both sequences were methylated in the original sequence. Methylation patterns have been implicated in aging, developmental biology, and cancer; however, there has been no simple and rapid method for determining the methylation pattern in genomic DNA. The method described in this paper is quick, simple, and accurate, and demonstrates an exciting application of capillary electrophoresis DNA sequencing.